March 18, 2017

Events and jobs

Research Fellow in Omics analysis – King’s College London – Apply by April 12, 2017

Postdoctoral Research Position in Marine Microbial Ecology – University of Southern Mississippi

General microbiome

Microbial Influences in Cardio–Metabolic Diseases – Rachel Petersen – New York Academy of Sciences

*Review: Microbiota: a key orchestrator of cancer therapy – Soumen Roy – Nature Reviews Cancer

*Review: Caenorhabditis elegans as a model for microbiome research – Fan Zhang – Frontiers in Microbiology

Human respiratory microbiome

The relationship between nasopharyngeal CCL5 and microbiota on disease severity among infants with bronchiolitis – Kohei Hasegawa – Allergy

Human gut microbiome

The Food Contaminant Deoxynivalenol Exacerbates the Genotoxicity of Gut Microbiota – Delphine Payros – mBio

Delayed utilization of some fast-fermenting soluble dietary fibers by human gut microbiota when presented in a mixture – Yunus E. Tuncil – Journal of Functional Foods

Animal experiments

Deciphering the combinatorial influence of diet and the microbiota on experimental colitis – Sean R. Llewellyn – bioRxiv

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish – Keaton Stagaman – ISME J

Animal microbiome

Comparison of bacterial populations in bedding material, on teat ends, and in milk of cows housed in compost bedded pack barns – R. L. Albino – Animal Production Science

Community analysis of microbial sharing and specialization in a Costa Rican ant–plant–hemipteran symbiosis – Elizabeth G. Pringle – Proceedings of the Royal Society Biological Sciences

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment – Till Röthig – Scientific Reports

Plant, root, and soil microbiome

Root microbiota drive direct integration of phosphate stress and immunity – Gabriel Castrillo – Nature

Striking alterations in the soil bacterial community structure and functioning of the biological N cycle induced by Pennisetum setaceum invasion in a semiarid environment – G. Rodríguez-Caballero – Soil Biology and Biochemistry

Plant growth promoting rhizobacteria are more effective under drought: a meta-analysis – Rachel L. Rubin – Plant and Soil

Effect of biodynamic soil amendments on microbial communities in comparison with inorganic fertilization – Sibylle Faust – Applied Soil Ecology

Water and extremophile microbiome

Bacterial diversity in fumarole environments of the Paricutín volcano, Michoacán (Mexico) – Miguel Medrano-Santillana – Extremophiles

Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica) – Rosabruna La Ferla – Microbial Ecology

Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data – Michelle A. Allen – Scientific Reports

A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater – Flavia Flaviani – Viruses

Built environment

Microbial dynamics in anaerobic digestion reactors for treating organic urban residues during the start-up process – Rocio J. Alcántara-Hernández – Letters in Applied Microbiology

Variability of airborne bacteria in an urban Mediterranean area (Thessaloniki, Greece) – Savvas Genitsaris – Atmospheric Environment

*Review: A review of microscopy and comparative molecular-based methods to characterize “Plastisphere” communities – Caroline De Tender – Analytical Methods


*Review: Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data – Jian Xu – Engineering

*Review: Metaproteomic strategies and applications for gut microbial research – Mingming Xiao – Applied Microbiology and Biotechnology

Microbes in the news

Bacteria-Enriched Lotion Battles Skin Infections – Jenna Flannigan – Live Science

Frozen, Freeze-dried Products for Fecal Microbiota Transplantation as Effective as Fresh? – Pharmacy Times

Study by Irish scientists finds porridge to be good for the heart and gut – RTE

Certain Bacteria Within Gut Microbiome May Halt Inflammation Naturally, Study Says – Patricia Inacio – IBD News Today

Antibiotic overuse might be bad for bees – Mary Beth Griggs – Popular Science

Microbiome research Studies aim to help health, environment – David Wahlberg – The Times Record

My cats poop for science – Jonathan M. Giltin – ars Technica

Microbes on the market

Seres doubles down on a microbiome do-over as the FDA clears a make-or-break study – John Carroll – Endpoint News

Bacteria Hysteria

Revealed: Which supermarket’s chicken is most likely to contain food poisoning bacteria? – Tom Belger – Liverpool Echo

February 20, 2017

This Monday we have some quite interesting news about microbes! Microbes found inside giant crystals in caves in Chihuahua, Mexico, may have survived there for tens of thousands of years, while meadows of underwater seagrass plants might lower levels of harmful bacteria in nearby ocean waters making the whole ecosystem — from corals to fish to humans — healthier. Enjoy your reading..

Pregnancy and early life

Adenoid bacterial colonization in a paediatric population – João Subtil – European Archives of Oto-Rhino-Laryngology

Human gut microbiome

Review: NLRP6: A Multifaceted Innate Immune Sensor – Maayan Levy – Trends in Immunology

Prebiotic inulin-type fructans induce specific changes in the human gut microbiota – Doris Vandeputte – Gut

Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy – Ruqi Tang – Gut

Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial – Sudarshan Paramsothy – The Lancet

Reinforcement of intestinal epithelial barrier by arabinoxylans in overweight and obese subjects: A randomized controlled trial: Arabinoxylans in gut barrier – Bouke N. Salden – Clinical Nutrition

Diet-induced obesity, gut microbiota and bone, including alveolar bone loss – Sathima Eaimworawuthikul – Archives of Oral Biology

Animal experiments

Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha Diversity – Robert S. Thompson – Frontiers in  Behavioral Neuroscience

Plant, root, and soil microbiome

Plant community and nitrogen deposition as drivers of α- and β-prokaryotic diversity in reconstructed oil-sands soils and natural boreal forest soils – Jacynthe Masse – Applied and Environmental Microbiology

Plant-microbial association in petroleum and gas exploration sites in the state of Assam, north-east India—significance for bioremediation – Hemen Sarma – Environmental Science and Pollution Research

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis – Sylwia Zielińska – Microbiology Open

Water and extremophile microbiome

Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes, and invertebrates – Joleah B. Lamb – Science

Phages and viruses

Cyanophage-encoded lipid-desaturases: oceanic distribution, diversity and function – Sheila Roitman – bioRxiv


Effects of gelling agent and extracellular signaling molecules on the culturability of marine bacteria – Anita Mac Rygaard – Applied and Environmental Microbiology

A tool named Iris for versatile high-throughput phenotyping in microorganisms – George Kritikos – Nature Microbiology

Microbes in the news 

Microbes survived inside giant cave crystals for up to 50,000 years – Science News

Three-way dance between herbivores, plants and microbes unveiled  –

Synthetic antibiotic developed by Sask. researchers to combat drug-resistant bacteria – CBC News

Salmonella ‘can kill cancer’: How bacteria that cause food poisoning could be used to attack tumour cells – Colin Fernandez for Daily Mail, UK

Brazilian peppertree packs power to knock out antibiotic-resistant bacteria – Science Daily

Bacteria Hysteria

Drug-resistant deadly bacteria more widespread than previously thought, study finds – News Medical


January 29, 2017

A post on fecal transplats, the gut microbiome of cranes, fungal diversity of soils, and much more.

Events and Jobs

Assistant Professor of Microbiology, Immunology & Tropical Medicine at George Washington University

General microbiome

The Stromal Intervention: Regulation of Immunity and Inflammation at the Epithelial-Mesenchymal Barrier – Roni Nowarski – Cell

Effect of adsorbants on in vitro biohydrogenation of 22:6n-3 by mixed cultures of rumen microorganisms – Marlene Escobar – Animal

Pregnancy and early life

Airway Microbial Community Turnover Differs by BPD Severity in Ventilated Preterm Infants – Brandie D. Wagner – PLoS One

Mode of Delivery and Its Influence on the Acquisition of Streptococcus mutans in Infants – Ritu G. Ubeja – International Journal of Clinical Pediatric Dentistry

Human gut microbiome

Blood Trimethylamine-N-Oxide Originates from Microbiota Mediated Breakdown of Phosphatidylcholine and Absorption from Small Intestine – Wolfgang Stremmel – PLoS One

Challenges in Fecal Donor Selection and Screening for Fecal Microbiota Transplantation: A Review – Michael H. Woodworth – Gut Microbes

Animal experiments

Peptostreptococcus anaerobius Induces Intracellular Cholesterol Biosynthesis in Colon Cells to Induce Proliferation and Causes Dysplasia in Mice – Ho Tsoi – Journal of AGA Institute: Gastroenterology Special Issure

Animal microbiome

The gut microbiome of hooded cranes (Grus monacha) wintering at Shengjin Lake, China – Guanghong Zhao – Wiley

Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters – Hooman Derakhashani – Frontiers in Microbiology

Effect of antibiotic on survival and development of Spodoptera litura (Lepidoptera: Noctuidae) and its gut microbial diversity – Abhinay Thakur – Bullitin of Entomological Research

Plant, root, and soil microbiome

Fungal diversity in soils across a gradient of preserved Brazilian Cerrado – Ademir Sergio Ferreira de Araujo – Journal of Microbiology

Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction – Stephanie G. Hays – Journal of Biomedical Engineering

Translocation of Bacillus thuringiensis in Phaseolus vulgaris tissues and vertical transmission in Arabidopsis thaliana – Rosalina García-Suárez – Journal of Applied Microbiology

Transport Capabilities of Environmental Pseudomonads for Sulfur Compounds – Sarah Zerbs – Protein Science

Water and extremophile microbiome

Molecular-biological sensing in aquatic environments: recent developments and emerging capabilities – Jonathan S McQuillan – Current Opinion in Biotechnology

Probiotics / prebiotics

Nutritional stimulation of commensal oral bacteria suppresses pathogens: the prebiotic concept – Vera Slomka – Wiley

Microbes in the news

Rebalancing gut microbiome lengthens survival in mouse model of ALS

What We’ve Learned From Studying Microbiomes

Microbiota Transfer Therapy Could Help Children With Autism

Bacteria’s sneaky way to spread by getting you to eat more

Studies show prevalence of multi-drug resistant bacteria in China

Researchers discover molecule that could fight ‘superbug’ bacteria

Microbes on the market

New Market Analysis: The global clinical microbiology market is projected to reach USD 5.77 Billion by 2021

Bacteria Hysteria

SHOCKING: You won’t BELIEVE how many GERMS are on your hands

January 5, 2017

Microbiome of Inuit, centenarians, microbes showing differential expression when they are grown with sound, taxonomy of prokaryotic viruses.

Human gut microbiome

Gut Microbiome of the Canadian Arctic Inuit – Catherine Girard – mSphere

The gut microbiota of centenarians: Signatures of longevity in the gut microbiota profile – Biagi Elena – Mechanisms of Ageing and Development

Review: Understanding the Molecular Mechanisms of the Interplay Between Herbal Medicines and Gut Microbiota – Jun Xu – Medicinal Research Reviews

Editorial: The microbiome as a source of new enterprises and job creation: Considering clinical faecal and synthetic microbiome transplants and therapeutic regulation – Daniel van der Lelie – Microbial Biotechnology

Animal experiments

Effect of dietary kefir on the growth performance, feed utilization and fatty acid profile of juvenile rainbow trout, Oncorhynchus mykiss – E. Gümüş – Aquaculture Nutrition

Plant, root, and soil microbiome

The Pseudomonas putida T6SS is a plant warden against phytopathogens – Patricia Bernal – The ISME Journal

Mycorrhizal Colonization Status and Rhizosphere Soil Properties of BCSIR Reserve Forest Rajshahi, Bangladesh – M. Halder – Current World Environment

Waste and pollution microbiology

Batch and continuous removal of heavy metals from industrial effluents using microbial consortia – F. Migahed – International Journal of Environmental Science and Technology

Musical microbes

Frequency-dependent response of Chromobacterium violaceum to sonic stimulation, and altered gene expression associated with enhanced violacein production at 300 Hz – Chinmayi Joshi – bioRxiv


Book: Molecular Data Analysis Using R – Csaba Ortutay

Viruses and phages

Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee – Evelien M. Adriaenssens – Archives of Virology


Optimal allocation of metabolic functions among organisms in a microbial ecosystem – Qi Zhao – Decision and Control (CDC), 2016 IEEE 55th Conference on

Microbes in the news

CDC keeps secret its mishaps with deadly germs: CDC blacked-out information from lab incident reports – Alison Young – USA Today

Single fecal transplant no more effective than standard of care in treating C. diff – MedicalXpress

Alaska gulls are picking up antibiotic-resistant bacteria that could infect humans – Yereth Rosen – ADN

Man-made lake near Linganore drained to kill toxic pink bacteria: pink-colored cyanobacterium releases a toxin – Samantha Hogan – The Frederick News Post

Bacteria Hysteria

Dirty Money. The public health case for a cashless society – Dina Fine Maron – Scientific American
The Money in Your Wallet Might Be Covered With Poop, Mold, and Cocaine – Brad
– Money
The 5 Dirtiest Things You Touch Every Day – Markham Heid – Time

Microbes in the market

Israeli Gut Microbiome Startup Lands Mayo Clinic Venture Backing – TwinCities Business

Ritter Pharmaceuticals Phase 2a Lactose Intolerance Clinical Trial Microbiome Data, Published in Proceedings of the National Academy of Sciences – Yahoo

Cambridge BioMarketing Announces Five Predictions for 2017 – Yahoo

Bruker Announces Acquisition of CMO InVivo Biotech to Expand Molecular Biology, Microbiology and Pathology Consumables and Assay Business – PR Newswire

Science integrity

Bavarian court sentences me to prison if I dare repeat unwelcome facts of Walles’ trachea transplants – Leonid Schneider – For Better Science


January 4, 2017

Short-chain sugars and lactose intolerance, NEC and bile salts, gut microbiome in women with Polycystic Ovary Syndrome, Brucella in frogs. And since this is a quiet time on the microbiome literature front,  I also included some other interesting microbes in the news.

Pregnancy and early life

Fecal Bile Salts and the Development of Necrotizing Enterocolitis in Preterm Infants – Christian V. Hulzebos – PLOS ONE

Human respiratory microbiome

Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation – Linh Do Ngoc Nguyen – PLOS ONE

Human gut microbiome

Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals – M. Andrea Azcarate-Peril – PNAS

Alterations in Gut Microbiome Composition and Barrier Function Are Associated with Reproductive and Metabolic Defects in Women with Polycystic Ovary Syndrome (PCOS): A Pilot Study – Lisa Lindheim – PLOS ONE

Review: Modulation of alloimmune response by commensal gut microbiota and potential new avenues to influence the outcome of allogeneic transplantation by modification of the ‘gut culture’ – S. Kanangat – International Journal of Immunogenetics

Editorial: Gut Microbiota, Diet and Health. (We and our gut microbes) – Juan Carlos Espín – Molecular Nutrition & Food Research

Editorial: Hot Topics in 2017 – Gut Microbiota, Whole Grains and Health – Hans-Ulrich Humpf – Molecular Nutrition & Food Research

Microbiology of nearly sterile sites

Pseudomonas aeruginosa Microcolonies in Coronary Thrombi from Patients with ST-Segment Elevation Myocardial Infarction – Gorm Mørk Hansen – PLOS ONE

Animal microbiome

The Change of a Medically Important Genus: Worldwide Occurrence of Genetically Diverse Novel Brucella Species in Exotic Frogs – Holger C. Scholz – PLOS ONE

Synbiotics for Broiler Chickens—In Vitro Design and Evaluation of the Influence on Host and Selected Microbiota Populations following In Ovo Delivery – Aleksandra Dunislawska – PLOS ONE

Plant, root, and soil microbiome

Frontiers for research on the ecology of plant-pathogenic bacteria: fundamentals for sustainability. Challenges in Bacterial Molecular Plant Pathology – Cindy E. Morris – Molecular Plant Pathology

Water and extremophile microbiome

Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment – Christophe Leboulanger – PLOS ONE

Food microbiology

Crystal Ball: Exciting strain-level resolution studies of the food microbiome – Danilo Ercolini – Microbial Biotechnology

Viruses / phages / bioinformatics / metagenomics

Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data – Guillaume Carissimo – PLOS ONE

Microbial Ecology

Effects of Spatial Localization on Microbial Consortia Growth – Michael Venters – PLOS ONE

More microbiology / Microbes in the news

RelA Mutant Enterococcus faecium with Multiantibiotic Tolerance Arising in an Immunocompromised Host– Erin S. Honsa – mBio

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins – Benjamin J. Rauch – Cell

50 Years of Journal of Virology: Classic Spotlight, 1969 and 1970: Articles of Significant Interest Selected from the Journal of Virology Archives by the Editors – Journal of Virology

Research Highlight: Building a bacterial ribosome – Ashley York – Nature Reviews Microbiology

Sepsis and Hemocyte Loss in Honey Bees (Apis mellifera) Infected with Serratia marcescens Strain Sicaria – Nancy L. Burritt – PLOS ONE

Switching of metabolic programs in response to light availability is an essential function of the cyanobacterial circadian clock – Anna M Puszynska – bioRxiv

Microbiomes Move Standard Plate Count One Step Forward – Gregory Siragusa – Food Safety Tech

Bisphenol-A Linked to Endocrine Disorders in Pets, Humans – CBS Local

Microbes on the market

Alimentary discoveries produce a gut reaction among investors – Companies aim to exploit one of the 21st century’s big advances – Clive Cookson – Financial Times

Marina Biotech Granted European Claims Covering Bacteria Mediated Gene Silencing – Market Wired

A Bright Future for Bacteria – Betsy Davis – Pharma Elsevier

Synthetic Biologics to Present at the Biotech Showcase™ 2017 Conference – PR Newswire

Bacteria Hysteria

The Bacteria We’ve Got to Beat: Nasty germs lurk on cell phones, doorknobs, ketchup bottles — here’s how to fight ’em this flu season – Carleen Wild – Lifezette

November 26, 2016

Human reproductive microbiome

Una destinatio, viae diversae: Does exposure to the vaginal microbiota confer health benefits to the infant, and does lack of exposure confer disease risk? – Kjersti Aagaard – EMBO Reports

Review: Female reproductive tract microbiome in gynecological health and problems – Shyamalina Haldar – Journal of Reproductive Health and Medicine

Animal microbiome

Bacterial diversity shift determined by different diets in the gut of the spotted wing fly Drosophila suzukii is primarily reflected on acetic acid bacteria – Violetta Vacchini – Environmental Microbiol Reports

Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis – Juliane Wippler – BMC Genomics

Microbial communities of lycaenid butterflies do not correlate with larval diet – Melissa Whitaker – Frontiers in Microbiology

Bees: Report on the microbiota of Melipona quadrifasciata affected by a recurrent disease – Sebastián Díaz – Journal of Invertebrate Pathology

Symbiont Diversity of Aphis (Toxoptera) citricidus (Hemiptera: Aphididae) as Influenced by Host Plants – Aline Sartori Guidolin – Microbial Ecology

Sponge Microbiota Are a Reservoir of Functional Antibiotic Resistance Genes – Dennis Versluis – Frontiers in Microbiology

Plant, root, and soil microbiome

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks – Eduardo Pérez-Valera –  Environmental Microbiology

Integrated Proteomics and Metabolomics Suggests Symbiotic Metabolism and Multimodal Regulation in a Fungal-Endobacterial System – Zhou Li – Environmental Microbiology

Water and extremophile microbiome

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient – C. Monard – Scientific Reports

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments – Sizhong Yang – Scientific Reports

Microbial Activity Response to Solar Radiation across Contrasting Environmental Conditions in Salar de Huasco, Northern Chilean Altiplano – Klaudia L. Hernández – Frontiers in Microbiology

Built environment / money microbiome

Dirty Money: A Matter of Bacterial Survival, Adherence, and Toxicity – Frank Vriesekoop – Microorganisms


Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes – Jeremy L. Motley – Journal of Natural Products


Note: human contamination in feces samples is usually low (e.g. compared to oral or vaginal samples; not really an issue in my opinion: An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction – Jitendra Kumar – Genomics, Proteomics & Bioinformatics

More microbiology

Independent evolution of shape and motility allows evolutionary flexibility in Firmicutes bacteria – Fouad El Baidouri – Nature Ecology & Evolution

Press: Reshaping our ideas of bacterial evolution – Science Daily

Microbes in the news

This paper is not yet available online at Molecular Biology and Evolution, but already some press about it:
A comprehensive tree of prokaryotic life – Science Daily
New insights from the most comprehensive tree of prokaryotic life assembled to date –

Bacteria taught to bond carbon and silicon for the first time – Aviva Rutkin – New Scientist

Binge-eating bacteria extract energy from sewage – Science Daily

Video: Good Germs; Bad Germs. Microbes in the kitchen, 14 households, 500 swabs – University of Oxford – YouTube

Bacteria Hysteria

Note: Sponsored by a company specialized in pest control and hygiene productsPrimary school bacteria leaves teachers at risk of sickness – TES

November 4, 2016

A very short Digest today, since Stanford unexpectedly closed my email account, so I cannot access most eTOCs. I had requested a couple of months extension, but it did not happen 😦   Here is what I found for you today:

Plant, root, and soil microbiome

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’ – Tess E. Brewer – Nature Microbiology

Mycorrhizal compatibility and symbiotic seed germination of orchids from the Coastal Range and Andes in south central Chile – Hector Herrera – Mycorrhiza

Microbes in the news

One of our reporters tried to do CRISPR. He failed miserably – Jon Cohen – Science

Polysorbate as possible E. coli food poisoning fix – Barfblog

Food Additive Could Treat E. Coli Food Poisoning – ValueWalk

A penguin in the Bombay Zoo that recently died: Dory’s death: one more test confirms bacterial infection – Tanvi Deshpande
Finding Dory’s killer? Authorities in no rush – Rupsa Chakraborty – Midday

Microbes on the market

OptiBiotix Health Plc Presentation of data at European Microbiome Summit – Directors Talk Interviews

Enterome Appoints Christophe Bonny as Chief Scientific Officer – PR Newswire


The dirt on phones: See what you’re holding in your hands – WIBW